Chlamydomonas reinhardtii is a model organism for fundamental discovery in photosynthesis and ciliary biology. Its genome is one of five flagship genomes at the Joint Genome Institute, indicative of their commitment to finishing and investment in infrastructure for maintaining the database. We will add value to the JGI effort by using transcriptome data, generated via RNA-seq methodology on lllumina's platform, to a) derive better gene models, b) identify differentially expressed genes and alternate transcript forms under various experimental conditions, and c) deduce the pattern of expression of every gene in the genome and the absolute abundance of every transcript. Although > 300,000 ESTs have been sequenced, only 59% of the ~16,000 gene models are supported by EST coverage, and only 21% have both 5' and 3' UTR information. Therefore, many gene models, both computationally predicted as well as homology-based are incorrect or at best incomplete. With RNA-seq approaches we obtain much greater coverage of the transcriptome, which can significantly elevate the quality of annotation. In any given condition, there is a range of four orders of magnitude for transcript abundance, but by increasing the number of runs we can sample even low abundance transcripts. Therefore, to increase the coverage of the transcriptome, transcript sequence data will be collected from cells grown under various environmental and physiological conditions, including variation in macro- and micro-nutrients, pH, temperature, light intensity, C02 and 02 partial pressures, and under different developmental situations (gametogenesis, zygote, cell wall and flagella regeneration). Each sample will be handled separately so that we can compare specific RNA abundance within and among each sample, which will elucidate transcription networks associated with specific environmental and developmental conditions. The primary sequence data will be deposited with associated metadata periodically at NCBI SRA and the derived data will be loaded onto a publicly accessible browser maintained at UCLA and periodically uploaded to Chlamybase and the JGI genome browser for long term public access.